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Bylino OV, Ogienko AA, Batin MA, Georgiev PG, Omelina ES. Genetic, Environmental, and Stochastic Components of Lifespan Variability: The Drosophila Paradigm. Int J Mol Sci 2024; 25:4482. [PMID: 38674068 PMCID: PMC11050664 DOI: 10.3390/ijms25084482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/25/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Lifespan is a complex quantitative trait involving genetic and non-genetic factors as well as the peculiarities of ontogenesis. As with all quantitative traits, lifespan shows considerable variation within populations and between individuals. Drosophila, a favourite object of geneticists, has greatly advanced our understanding of how different forms of variability affect lifespan. This review considers the role of heritable genetic variability, phenotypic plasticity and stochastic variability in controlling lifespan in Drosophila melanogaster. We discuss the major historical milestones in the development of the genetic approach to study lifespan, the breeding of long-lived lines, advances in lifespan QTL mapping, the environmental factors that have the greatest influence on lifespan in laboratory maintained flies, and the mechanisms, by which individual development affects longevity. The interplay between approaches to study ageing and lifespan limitation will also be discussed. Particular attention will be paid to the interaction of different types of variability in the control of lifespan.
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Affiliation(s)
- Oleg V. Bylino
- Department of Regulation of Genetic Processes, Laboratory of Molecular Organization of the Genome, Institute of Gene Biology RAS, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anna A. Ogienko
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Mikhail A. Batin
- Open Longevity, 15260 Ventura Blvd., Sherman Oaks, Los Angeles, CA 91403, USA
| | - Pavel G. Georgiev
- Department of Regulation of Genetic Processes, Laboratory of Molecular Organization of the Genome, Institute of Gene Biology RAS, 119334 Moscow, Russia
| | - Evgeniya S. Omelina
- Department of Regulation of Genetic Processes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
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Unraveling the Role of Antimicrobial Peptides in Insects. Int J Mol Sci 2023; 24:ijms24065753. [PMID: 36982826 PMCID: PMC10059942 DOI: 10.3390/ijms24065753] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Antimicrobial peptides (AMPs) are short, mainly positively charged, amphipathic molecules. AMPs are important effectors of the immune response in insects with a broad spectrum of antibacterial, antifungal, and antiparasitic activity. In addition to these well-known roles, AMPs exhibit many other, often unobvious, functions in the host. They support insects in the elimination of viral infections. AMPs participate in the regulation of brain-controlled processes, e.g., sleep and non-associative learning. By influencing neuronal health, communication, and activity, they can affect the functioning of the insect nervous system. Expansion of the AMP repertoire and loss of their specificity is connected with the aging process and lifespan of insects. Moreover, AMPs take part in maintaining gut homeostasis, regulating the number of endosymbionts as well as reducing the number of foreign microbiota. In turn, the presence of AMPs in insect venom prevents the spread of infection in social insects, where the prey may be a source of pathogens.
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Pegoraro M, Fishman B, Zonato V, Zouganelis G, Francis A, Kyriacou CP, Tauber E. Photoperiod-Dependent Expression of MicroRNA in Drosophila. Int J Mol Sci 2022; 23:ijms23094935. [PMID: 35563325 PMCID: PMC9100521 DOI: 10.3390/ijms23094935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 12/07/2022] Open
Abstract
Like many other insects in temperate regions, Drosophila melanogaster exploits the photoperiod shortening that occurs during the autumn as an important cue to trigger a seasonal response. Flies survive the winter by entering a state of reproductive arrest (diapause), which drives the relocation of resources from reproduction to survival. Here, we profiled the expression of microRNA (miRNA) in long and short photoperiods and identified seven differentially expressed miRNAs (dme-mir-2b, dme-mir-11, dme-mir-34, dme-mir-274, dme-mir-184, dme-mir-184*, and dme-mir-285). Misexpression of dme-mir-2b, dme-mir-184, and dme-mir-274 in pigment-dispersing, factor-expressing neurons largely disrupted the normal photoperiodic response, suggesting that these miRNAs play functional roles in photoperiodic timing. We also analyzed the targets of photoperiodic miRNA by both computational predication and by Argonaute-1-mediated immunoprecipitation of long- and short-day RNA samples. Together with global transcriptome profiling, our results expand existing data on other Drosophila species, identifying genes and pathways that are differentially regulated in different photoperiods and reproductive status. Our data suggest that post-transcriptional regulation by miRNA is an important facet of photoperiodic timing.
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Affiliation(s)
- Mirko Pegoraro
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (M.P.); (A.F.)
| | - Bettina Fishman
- Department of Evolutionary & Environmental Biology, Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Valeria Zonato
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (V.Z.); (C.P.K.)
| | | | - Amanda Francis
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK; (M.P.); (A.F.)
| | - Charalambos P. Kyriacou
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (V.Z.); (C.P.K.)
| | - Eran Tauber
- Department of Evolutionary & Environmental Biology, Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
- Correspondence:
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Weeraratne TC, Karunaratne SHPP, Reimer L, de Silva WAPP, Wondji CS. Use of transcriptional age grading technique to determine the chronological age of Sri Lankan Aedes aegypti and Aedes albopictus females. Parasit Vectors 2021; 14:493. [PMID: 34565445 PMCID: PMC8474866 DOI: 10.1186/s13071-021-04994-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aedes aegypti and Ae. albopictus are important vectors of human diseases such as dengue, chikungunya, and zika. In Sri Lanka, they have been responsible for transmitting dengue virus. One of the most important parameters influencing the likelihood of arbovirus transmission is the age structure of the mosquito population. However, mosquito age is difficult to measure with accuracy. This study aims to construct multivariate calibration models using the transcriptional abundance of three age-responsive genes: Ae15848 (calcium-binding protein), Ae8505 (structural component of cuticle), and Ae4274 (fizzy cell cycle/cell division cycle 20). METHODS The transcriptional age-grading technique was applied to determine the chronological age of Ae. aegypti and Ae. albopictus female mosquito populations from Sri Lanka using the age-responsive genes Ae15848, Ae8505, and Ae4274. Furthermore, Ae. aegypti samples obtained from colonies reared at two temperatures (23 and 27 °C) were used to investigate the influence of temperature on this age-grading technique. Expression levels of these three genes were quantified using reverse transcription qualitative PCR (qRT-PCR), and results were normalized against the housekeeping gene ribosomal gene S17 (RpS17). RESULTS The expression of Ae15848 and Ae8505 decreased with the age of mosquitoes and showed the most significant and consistent change while expression of Ae4274 increased with age. The multivariate calibration models showed > 80% correlation between expression of these age-responsive genes and the age of female mosquitoes at both temperatures. At 27 °C the accuracy of age predictions using the models was 2.19 (± 1.66) days and 2.58 (± 2.06) days for Ae. aegypti and Ae. albopictus females, respectively. The accuracy of the model for Ae. aegypti at 23 °C was 3.42 (± 2.74) days. CONCLUSIONS An adult rearing temperature difference of 4 °C (23-27 °C) did not significantly affect the age predictions. The calibration models created during this study could be successfully used to estimate the age of wild Ae. aegypti and Ae. albopictus mosquitoes from Sri Lanka.
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Affiliation(s)
| | | | - Lisa Reimer
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | | | - Charles S Wondji
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.,Medical Entomology Department, Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
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Costa CP, Duennes MA, Fisher K, Der JP, Watrous KM, Okamoto N, Yamanaka N, Woodard SH. Transcriptome analysis reveals nutrition‐ and age‐related patterns of gene expression in the fat body of pre‐overwintering bumble bee queens. Mol Ecol 2020; 29:720-737. [DOI: 10.1111/mec.15361] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 01/01/2023]
Affiliation(s)
| | | | - Kaleigh Fisher
- Department of Entomology University of California Riverside CA USA
| | - Joshua P. Der
- Department of Biological Science California State University Fullerton CA USA
| | | | - Naoki Okamoto
- Department of Entomology University of California Riverside CA USA
| | - Naoki Yamanaka
- Department of Entomology University of California Riverside CA USA
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Knockdown of the neuronal gene Lim3 at the early stages of development affects mitochondrial function and lifespan in Drosophila. Mech Ageing Dev 2019; 181:29-41. [DOI: 10.1016/j.mad.2019.111121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 04/29/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023]
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Monroy Kuhn JM, Meusemann K, Korb J. Long live the queen, the king and the commoner? Transcript expression differences between old and young in the termite Cryptotermes secundus. PLoS One 2019; 14:e0210371. [PMID: 30759161 PMCID: PMC6373952 DOI: 10.1371/journal.pone.0210371] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 12/20/2018] [Indexed: 01/09/2023] Open
Abstract
Social insects provide promising new avenues for aging research. Within a colony, individuals that share the same genetic background can differ in lifespan by up to two orders of magnitude. Reproducing queens (and in termites also kings) can live for more than 20 years, extraordinary lifespans for insects. We studied aging in a termite species, Cryptotermes secundus, which lives in less socially complex societies with a few hundred colony members. Reproductives develop from workers which are totipotent immatures. Comparing transcriptomes of young and old individuals, we found evidence for aging in reproductives that was especially associated with DNA and protein damage and the activity of transposable elements. By contrast, workers seemed to be better protected against aging. Thus our results differed from those obtained for social insects that live in more complex societies. Yet, they are in agreement with lifespan estimates for the study species. Our data are also in line with expectations from evolutionary theory. For individuals that are able to reproduce, it predicts that aging should only start after reaching maturity. As C. secundus workers are immatures with full reproductive options we expect them to invest into anti-aging processes. Our study illustrates that the degree of aging can differ between social insects and that it may be associated with caste-specific opportunities for reproduction.
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Affiliation(s)
- José Manuel Monroy Kuhn
- Evolutionary Biology and Ecology, Albert-Ludwigs-Universität Freiburg, Freiburg, Baden-Württemberg, Germany
- * E-mail: (JMMK); (JK)
| | - Karen Meusemann
- Evolutionary Biology and Ecology, Albert-Ludwigs-Universität Freiburg, Freiburg, Baden-Württemberg, Germany
| | - Judith Korb
- Evolutionary Biology and Ecology, Albert-Ludwigs-Universität Freiburg, Freiburg, Baden-Württemberg, Germany
- * E-mail: (JMMK); (JK)
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Spurrier J, Shukla AK, McLinden K, Johnson K, Giniger E. Altered expression of the Cdk5 activator-like protein, Cdk5α, causes neurodegeneration, in part by accelerating the rate of aging. Dis Model Mech 2018; 11:dmm031161. [PMID: 29469033 PMCID: PMC5897722 DOI: 10.1242/dmm.031161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 02/02/2018] [Indexed: 12/11/2022] Open
Abstract
Aging is the greatest risk factor for neurodegeneration, but the connection between the two processes remains opaque. This is in part for want of a rigorous way to define physiological age, as opposed to chronological age. Here, we develop a comprehensive metric for physiological age in Drosophila, based on genome-wide expression profiling. We applied this metric to a model of adult-onset neurodegeneration, increased or decreased expression of the activating subunit of the Cdk5 protein kinase, encoded by the gene Cdk5α, the ortholog of mammalian p35. Cdk5α-mediated degeneration was associated with a 27-150% acceleration of the intrinsic rate of aging, depending on the tissue and genetic manipulation. Gene ontology analysis and direct experimental tests revealed that affected age-associated processes included numerous core phenotypes of neurodegeneration, including enhanced oxidative stress and impaired proteostasis. Taken together, our results suggest that Cdk5α-mediated neurodegeneration results from accelerated aging, in combination with cell-autonomous neuronal insults. These data fundamentally recast our picture of the relationship between neurodegeneration and its most prominent risk factor, natural aging.
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Affiliation(s)
- Joshua Spurrier
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 02892, USA
- The Johns Hopkins University/National Institutes of Health Graduate Partnership Program, National Institutes of Health, Bethesda, MD 02892, USA
| | - Arvind Kumar Shukla
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 02892, USA
| | - Kristina McLinden
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 02892, USA
| | - Kory Johnson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 02892, USA
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 02892, USA
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Abstract
Here, we provide a brief review of the mechanistic connections between immunity and aging—a fundamental biological relationship that remains poorly understood—by considering two intertwined questions: how does aging affect immunity, and how does immunity affect aging? On the one hand, aging contributes to the deterioration of immune function and predisposes the organism to infections (“immuno-senescence”). On the other hand, excessive activation of the immune system can accelerate degenerative processes, cause inflammation and immunopathology, and thus promote aging (“inflammaging”). Interestingly, several recent lines of evidence support the hypothesis that restrained or curbed immune activity at old age (that is, optimized age-dependent immune homeostasis) might actually improve realized immune function and thereby promote longevity. We focus mainly on insights from
Drosophila, a powerful genetic model system in which both immunity and aging have been extensively studied, and conclude by outlining several unresolved questions in the field.
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Affiliation(s)
- Kathrin Garschall
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland
| | - Thomas Flatt
- Department of Ecology & Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
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Yu S, Lee E, Tsogbadrakh B, Son GI, Kim M. Prenatal hyperbaric normoxia treatment improves healthspan and regulates chitin metabolic genes in Drosophila melanogaster. Aging (Albany NY) 2017; 8:2538-2550. [PMID: 27777382 PMCID: PMC5115905 DOI: 10.18632/aging.101084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 10/10/2016] [Indexed: 12/30/2022]
Abstract
Aging is a universal, irreversible process accompanied by physiological declines that culminate in death. Rapid progress in gerontology research has revealed that aging can be slowed through mild stress-induced hormesis. We previously reported that hyperbaric normoxia (HN, 2 atm absolute pressure with 10% O2) induces a cytoprotective response in vitro by regulating fibronectin. In the present study, we investigated the hormetic effects of prenatal HN exposure on Drosophila healthspan related to molecular defense mechanisms. HN exposure had no disruptive effect on developmental rate or adult body weight. However, lifespan was clearly enhanced, as was resistance to oxidative and heat stress. In addition, levels of reactive oxygen species were significantly decreased and motor performance was increased. HN stress has been shown to trigger molecular changes in the heat shock response and ROS scavenging system, including hsp70, catalase, glutathione synthase, and MnSOD. Furthermore, to determine the hormetic mechanism underlying these phenotypic and molecular changes, we performed a genome-wide profiling in HN-exposed and control flies. Genes encoding chitin metabolism were highly up-regulated, which could possibly serve to scavenge free radicals. These results identify prenatal HN exposure as a potential hormetic factor that may improve longevity and healthspan by enhancing defense mechanisms in Drosophila.
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Affiliation(s)
- Suyeun Yu
- Department of Preventive Medicine, College of Medicine, Korea University, Seoul, 136-701, Republic of Korea
| | - Eunil Lee
- Department of Preventive Medicine, College of Medicine, Korea University, Seoul, 136-701, Republic of Korea
| | - Bodokhsuren Tsogbadrakh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, 151-742, Republic of Korea
| | - Gwang-Ic Son
- Department of Preventive Medicine, College of Medicine, Korea University, Seoul, 136-701, Republic of Korea
| | - Mari Kim
- Department of Preventive Medicine, College of Medicine, Korea University, Seoul, 136-701, Republic of Korea
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Des Marteaux LE, McKinnon AH, Udaka H, Toxopeus J, Sinclair BJ. Effects of cold-acclimation on gene expression in Fall field cricket (Gryllus pennsylvanicus) ionoregulatory tissues. BMC Genomics 2017; 18:357. [PMID: 28482796 PMCID: PMC5422886 DOI: 10.1186/s12864-017-3711-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 04/20/2017] [Indexed: 11/13/2022] Open
Abstract
Background Cold tolerance is a key determinant of temperate insect distribution and performance. Chill-susceptible insects lose ion and water homeostasis during cold exposure, but prior cold acclimation improves both cold tolerance and defense of homeostasis. The mechanisms underlying these processes are mostly unknown; cold acclimation is thought to enhance ion transport in the cold and/or prevent leak of water and ions. To identify candidate mechanisms of cold tolerance plasticity we generated transcriptomes of ionoregulatory tissues (hindgut and Malpighian tubules) from Gryllus pennsylvanicus crickets and compared gene expression in warm- and cold-acclimated individuals. Results We assembled a G. pennsylvanicus transcriptome de novo from 286 million 50-bp reads, yielding 70,037 contigs (~44% of which had putative BLAST identities). We compared the transcriptomes of warm- and cold-acclimated hindguts and Malpighian tubules. Cold acclimation led to a ≥ 2-fold change in the expression of 1493 hindgut genes (733 downregulated, 760 upregulated) and 2008 Malpighian tubule genes (1009 downregulated, 999 upregulated). Cold-acclimated crickets had altered expression of genes putatively associated with ion and water balance, including: a downregulation of V-ATPase and carbonic anhydrase in the Malpighian tubules and an upregulation of Na+-K+ ATPase in the hindgut. We also observed acclimation-related shifts in the expression of cytoskeletal genes in the hindgut, including actin and actin-anchoring/stabilizing proteins, tubulin, α-actinin, and genes involved in adherens junctions organization. In both tissues, cold acclimation led to differential expression of genes encoding cytochrome P450s, glutathione-S-transferases, apoptosis factors, DNA repair, and heat shock proteins. Conclusions This is the first G. pennsylvanicus transcriptome, and our tissue-specific approach yielded new candidate mechanisms of cold tolerance plasticity. Cold acclimation may reduce loss of hemolymph volume in the cold by 1) decreasing primary urine production via reduced expression of carbonic anhydrase and V-ATPase in the Malpighian tubules and 2) by increasing Na+ (and therefore water) reabsorption across the hindgut via increase in Na+-K+ ATPase expression. Cold acclimation may reduce chilling injury by remodeling and stabilizing the hindgut epithelial cytoskeleton and cell-to-cell junctions, and by increasing the expression of genes involved in DNA repair, detoxification, and protein chaperones. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3711-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Alexander H McKinnon
- Department of Biology, The University of Western Ontario, London, ON, Canada.,Present Address: Faculty of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Hiroko Udaka
- Department of Biology, The University of Western Ontario, London, ON, Canada.,Present Address: Graduate School of Science, Biological Sciences, Kyoto University, Kyoto, Japan
| | - Jantina Toxopeus
- Department of Biology, The University of Western Ontario, London, ON, Canada
| | - Brent J Sinclair
- Department of Biology, The University of Western Ontario, London, ON, Canada
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Highfill CA, Reeves GA, Macdonald SJ. Genetic analysis of variation in lifespan using a multiparental advanced intercross Drosophila mapping population. BMC Genet 2016; 17:113. [PMID: 27485207 PMCID: PMC4970266 DOI: 10.1186/s12863-016-0419-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Considerable natural variation for lifespan exists within human and animal populations. Genetically dissecting this variation can elucidate the pathways and genes involved in aging, and help uncover the genetic mechanisms underlying risk for age-related diseases. Studying aging in model systems is attractive due to their relatively short lifespan, and the ability to carry out programmed crosses under environmentally-controlled conditions. Here we investigate the genetic architecture of lifespan using the Drosophila Synthetic Population Resource (DSPR), a multiparental advanced intercross mapping population. RESULTS We measured lifespan in females from 805 DSPR lines, mapping five QTL (Quantitative Trait Loci) that each contribute 4-5 % to among-line lifespan variation in the DSPR. Each of these QTL co-localizes with the position of at least one QTL mapped in 13 previous studies of lifespan variation in flies. However, given that these studies implicate >90 % of the genome in the control of lifespan, this level of overlap is unsurprising. DSPR QTL intervals harbor 11-155 protein-coding genes, and we used RNAseq on samples of young and old flies to help resolve pathways affecting lifespan, and identify potentially causative loci present within mapped QTL intervals. Broad age-related patterns of expression revealed by these data recapitulate results from previous work. For example, we see an increase in antimicrobial defense gene expression with age, and a decrease in expression of genes involved in the electron transport chain. Several genes within QTL intervals are highlighted by our RNAseq data, such as Relish, a critical immune response gene, that shows increased expression with age, and UQCR-14, a gene involved in mitochondrial electron transport, that has reduced expression in older flies. CONCLUSIONS The five QTL we isolate collectively explain a considerable fraction of the genetic variation for female lifespan in the DSPR, and implicate modest numbers of genes. In several cases the candidate loci we highlight reside in biological pathways already implicated in the control of lifespan variation. Thus, our results provide further evidence that functional genetics tests targeting these genes will be fruitful, lead to the identification of natural sequence variants contributing to lifespan variation, and help uncover the mechanisms of aging.
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Affiliation(s)
- Chad A Highfill
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
| | - G Adam Reeves
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA
| | - Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA. .,Center for Computational Biology, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA.
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13
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Parkhitko AA, Binari R, Zhang N, Asara JM, Demontis F, Perrimon N. Tissue-specific down-regulation of S-adenosyl-homocysteine via suppression of dAhcyL1/dAhcyL2 extends health span and life span in Drosophila. Genes Dev 2016; 30:1409-22. [PMID: 27313316 PMCID: PMC4926864 DOI: 10.1101/gad.282277.116] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/17/2016] [Indexed: 12/16/2022]
Abstract
Methionine generates the methyl donor SAM, which is converted via methylation to SAH, which accumulates during aging. Parkhitko et al. discovered significant life span extension in response to down-regulation of two noncanonical Drosophila homologs of the SAH hydrolase Ahcy, CG9977/dAhcyL1 and Ahcy89E/CG8956/dAhcyL2, which act as dominant-negative regulators of canonical AHCY. Tissue-specific down-regulation of dAhcyL1/L2 in the brain and intestine extends health and life span. Aging is a risk factor for many human pathologies and is characterized by extensive metabolic changes. Using targeted high-throughput metabolite profiling in Drosophila melanogaster at different ages, we demonstrate that methionine metabolism changes strikingly during aging. Methionine generates the methyl donor S-adenosyl-methionine (SAM), which is converted via methylation to S-adenosyl-homocysteine (SAH), which accumulates during aging. A targeted RNAi screen against methionine pathway components revealed significant life span extension in response to down-regulation of two noncanonical Drosophila homologs of the SAH hydrolase Ahcy (S-adenosyl-L-homocysteine hydrolase [SAHH[), CG9977/dAhcyL1 and Ahcy89E/CG8956/dAhcyL2, which act as dominant-negative regulators of canonical AHCY. Importantly, tissue-specific down-regulation of dAhcyL1/L2 in the brain and intestine extends health and life span. Furthermore, metabolomic analysis of dAhcyL1-deficient flies revealed its effect on age-dependent metabolic reprogramming and H3K4 methylation. Altogether, reprogramming of methionine metabolism in young flies and suppression of age-dependent SAH accumulation lead to increased life span. These studies highlight the role of noncanonical Ahcy enzymes as determinants of healthy aging and longevity.
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Affiliation(s)
- Andrey A Parkhitko
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Richard Binari
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Nannan Zhang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; MOE Key Laboratory of Protein Sciences, Department of Pharmacology, School of Medicine, Tsinghua University, Beijing 100084, China
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, Division of Developmental Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
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Kučerová L, Kubrak OI, Bengtsson JM, Strnad H, Nylin S, Theopold U, Nässel DR. Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster. BMC Genomics 2016; 17:50. [PMID: 26758761 PMCID: PMC4711038 DOI: 10.1186/s12864-016-2383-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 01/06/2016] [Indexed: 12/28/2022] Open
Abstract
Background In models extensively used in studies of aging and extended lifespan, such as C. elegans and Drosophila, adult senescence is regulated by gene networks that are likely to be similar to ones that underlie lifespan extension during dormancy. These include the evolutionarily conserved insulin/IGF, TOR and germ line-signaling pathways. Dormancy, also known as dauer stage in the larval worm or adult diapause in the fly, is triggered by adverse environmental conditions, and results in drastically extended lifespan with negligible senescence. It is furthermore characterized by increased stress resistance and somatic maintenance, developmental arrest and reallocated energy resources. In the fly Drosophila melanogaster adult reproductive diapause is additionally manifested in arrested ovary development, improved immune defense and altered metabolism. However, the molecular mechanisms behind this adaptive lifespan extension are not well understood. Results A genome wide analysis of transcript changes in diapausing D. melanogaster revealed a differential regulation of more than 4600 genes. Gene ontology (GO) and KEGG pathway analysis reveal that many of these genes are part of signaling pathways that regulate metabolism, stress responses, detoxification, immunity, protein synthesis and processes during aging. More specifically, gene readouts and detailed mapping of the pathways indicate downregulation of insulin-IGF (IIS), target of rapamycin (TOR) and MAP kinase signaling, whereas Toll-dependent immune signaling, Jun-N-terminal kinase (JNK) and Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathways are upregulated during diapause. Furthermore, we detected transcriptional regulation of a large number of genes specifically associated with aging and longevity. Conclusions We find that many affected genes and signal pathways are shared between dormancy, aging and lifespan extension, including IIS, TOR, JAK/STAT and JNK. A substantial fraction of the genes affected by diapause have also been found to alter their expression in response to starvation and cold exposure in D. melanogaster, and the pathways overlap those reported in GO analysis of other invertebrates in dormancy or even hibernating mammals. Our study, thus, shows that D. melanogaster is a genetically tractable model for dormancy in other organisms and effects of dormancy on aging and lifespan. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2383-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lucie Kučerová
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm, Sweden.
| | - Olga I Kubrak
- Department of Zoology, Stockholm University, S-106 91, Stockholm, Sweden.
| | - Jonas M Bengtsson
- Department of Zoology, Stockholm University, S-106 91, Stockholm, Sweden.
| | - Hynek Strnad
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | - Sören Nylin
- Department of Zoology, Stockholm University, S-106 91, Stockholm, Sweden.
| | - Ulrich Theopold
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm, Sweden.
| | - Dick R Nässel
- Department of Zoology, Stockholm University, S-106 91, Stockholm, Sweden.
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15
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Carnes MU, Campbell T, Huang W, Butler DG, Carbone MA, Duncan LH, Harbajan SV, King EM, Peterson KR, Weitzel A, Zhou S, Mackay TFC. The Genomic Basis of Postponed Senescence in Drosophila melanogaster. PLoS One 2015; 10:e0138569. [PMID: 26378456 PMCID: PMC4574564 DOI: 10.1371/journal.pone.0138569] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/01/2015] [Indexed: 12/30/2022] Open
Abstract
Natural populations harbor considerable genetic variation for lifespan. While evolutionary theory provides general explanations for the existence of this variation, our knowledge of the genes harboring naturally occurring polymorphisms affecting lifespan is limited. Here, we assessed the genetic divergence between five Drosophila melanogaster lines selected for postponed senescence for over 170 generations (O lines) and five lines from the same base population maintained at a two week generation interval for over 850 generations (B lines). On average, O lines live 70% longer than B lines, are more productive at all ages, and have delayed senescence for other traits than reproduction. We performed population sequencing of pools of individuals from all B and O lines and identified 6,394 genetically divergent variants in or near 1,928 genes at a false discovery rate of 0.068. A 2.6 Mb region at the tip of the X chromosome contained many variants fixed for alternative alleles in the two populations, suggestive of a hard selective sweep. We also assessed genome wide gene expression of O and B lines at one and five weeks of age using RNA sequencing and identified genes with significant (false discovery rate < 0.05) effects on gene expression with age, population and the age by population interaction, separately for each sex. We identified transcripts that exhibited the transcriptional signature of postponed senescence and integrated the gene expression and genetic divergence data to identify 98 (175) top candidate genes in females (males) affecting postponed senescence and increased lifespan. While several of these genes have been previously associated with Drosophila lifespan, most are novel and constitute a rich resource for future functional validation.
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Affiliation(s)
- Megan Ulmer Carnes
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Terry Campbell
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Wen Huang
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America; Program in Genetics, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Daniel G Butler
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Mary Anna Carbone
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America; Program in Genetics, North Carolina State University, Raleigh, North Carolina, 27695, United States of America; W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Laura H Duncan
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Sasha V Harbajan
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Edward M King
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Kara R Peterson
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Alexander Weitzel
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Shanshan Zhou
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America; Program in Genetics, North Carolina State University, Raleigh, North Carolina, 27695, United States of America; W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
| | - Trudy F C Mackay
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, United States of America; Program in Genetics, North Carolina State University, Raleigh, North Carolina, 27695, United States of America; W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, 27695, United States of America
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16
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Geng T, Guan X, Smith EJ. Screening for genes involved in antibody response to sheep red blood cells in the chicken, Gallus gallus. Poult Sci 2015. [PMID: 26217034 DOI: 10.3382/ps/pev224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibody response, an important trait in both agriculture and biomedicine, plays a part in protecting animals from infection. Dissecting molecular basis of antibody response may improve artificial selection for natural disease resistance in livestock and poultry. A number of genetic markers associated with antibody response have been identified in the chicken and mouse by linkage-based association studies, which only define genomic regions by genetic markers but do not pinpoint genes for antibody response. In contrast, global expression profiling has been applied to define the molecular bases of a variety of biological traits through identification of differentially expressed genes (DEGs). Here, we employed Affimetrix GeneChip Chicken Genome Arrays to identify differentially expressed genes for antibody response to sheep red blood cells (SRBC) using chickens challenged with and without SRBC or chickens with high and low anti-SRBC titers. The DEGs include those with known (i.e., MHC class I and IgH genes) or unknown function in antibody response. Classification test of these genes suggested that the response of the chicken to intravenous injection of SRBC involved multiple biological processes, including response to stress or other different stimuli, sugar, carbohydrate or protein binding, and cell or soluble fraction, in addition to antibody response. This preliminary study thus provides an insight into molecular basis of antibody response to SRBC in the chicken.
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Affiliation(s)
- Tuoyu Geng
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, China College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, United States of America
| | - Xiaojing Guan
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, United States of America
| | - Edward J Smith
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, United States of America
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17
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Genome-Wide Gene Expression in relation to Age in Large Laboratory Cohorts of Drosophila melanogaster. GENETICS RESEARCH INTERNATIONAL 2015; 2015:835624. [PMID: 26090231 PMCID: PMC4454753 DOI: 10.1155/2015/835624] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 04/02/2015] [Accepted: 04/02/2015] [Indexed: 12/31/2022]
Abstract
Aging is a complex process characterized by a steady decline in an organism's ability to perform life-sustaining tasks. In the present study, two cages of approximately 12,000 mated Drosophila melanogaster females were used as a source of RNA from individuals sampled frequently as a function of age. A linear model for microarray data method was used for the microarray analysis to adjust for the box effect; it identified 1,581 candidate aging genes. Cluster analyses using a self-organizing map algorithm on the 1,581 significant genes identified gene expression patterns across different ages. Genes involved in immune system function and regulation, chorion assembly and function, and metabolism were all significantly differentially expressed as a function of age. The temporal pattern of data indicated that gene expression related to aging is affected relatively early in life span. In addition, the temporal variance in gene expression in immune function genes was compared to a random set of genes. There was an increase in the variance of gene expression within each cohort, which was not observed in the set of random genes. This observation is compatible with the hypothesis that D. melanogaster immune function genes lose control of gene expression as flies age.
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18
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Zhou S, Mackay TFC, Anholt RRH. Transcriptional and epigenetic responses to mating and aging in Drosophila melanogaster. BMC Genomics 2014; 15:927. [PMID: 25344338 PMCID: PMC4221674 DOI: 10.1186/1471-2164-15-927] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/13/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Phenotypic plasticity allows organisms to respond rapidly to changing environmental circumstances, and understanding its genomic basis can yield insights regarding the underlying genes and genetic networks affecting complex phenotypes. Female Drosophila melanogaster undergo dramatic physiological changes mediated by seminal fluid components transferred upon mating, including decreased longevity. Their physiological and behavioral effects have been well characterized, but little is known about resulting changes in regulation of gene expression or the extent to which mating-induced changes in gene expression are the same as those occurring during aging. RESULTS We assessed genome-wide mRNA, microRNA, and three common histone modifications implicated in gene activation for young and aged virgin and mated female D. melanogaster in a factorial design. We identified phenotypically plastic transcripts and epigenetic modifications associated with mating and aging. We used these data to derive phenotypically plastic regulatory networks associated with mating of young flies, and aging of virgin and mated flies. Many of the mRNAs, microRNAs and epigenetic modifications associated with mating of young flies also occur with age in virgin flies, which may reflect mating-induced accelerated aging. We functionally tested the plastic regulatory networks by overexpressing environmentally sensitive microRNAs. Overexpression resulted in altered expression of ~70% of candidate target genes, and in all cases affected oviposition. CONCLUSIONS Our results implicate microRNAs as mediators of phenotypic plasticity associated with mating and provide a comprehensive documentation of the genomic and epigenomic changes that accompany mating- and aging-induced physiological changes in female D. melanogaster.
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Affiliation(s)
| | | | - Robert R H Anholt
- Department of Biological Sciences, W, M, Keck Center for Behavioral Biology and Program in Genetics, Box 7614, North Carolina State University, Raleigh, NC 27695-7617, USA.
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19
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Liu J, Zhang Z, Rozovsky S. Selenoprotein K form an intermolecular diselenide bond with unusually high redox potential. FEBS Lett 2014; 588:3311-21. [PMID: 25117454 DOI: 10.1016/j.febslet.2014.07.037] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/17/2014] [Accepted: 07/22/2014] [Indexed: 11/16/2022]
Abstract
Selenoprotein K (SelK) is a membrane protein involved in antioxidant defense, calcium regulation and the ER-associated protein degradation pathway. We found that SelK exhibits a peroxidase activity with a rate that is low but within the range of other peroxidases. Notably, SelK reduced hydrophobic substrates, such as phospholipid hydroperoxides, which damage membranes. Thus, SelK might be involved in membrane repair or related pathways. SelK was also found to contain a diselenide bond-the first intramolecular bond of that kind reported for a selenoprotein. The redox potential of SelK was -257 mV, significantly higher than that of diselenide bonds in small molecules or proteins. Consequently, SelK can be reduced by thioredoxin reductase. These finding are essential for understanding SelK activity and function.
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Affiliation(s)
- Jun Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Zhengqi Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States.
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20
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Ayyadevara S, Tazearslan C, Alla R, Jiang JC, Jazwinski SM, Shmookler Reis RJ. Rec-8 dimorphism affects longevity, stress resistance and X-chromosome nondisjunction in C. elegans, and replicative lifespan in S. cerevisiae. Front Genet 2014; 5:211. [PMID: 25136348 PMCID: PMC4120681 DOI: 10.3389/fgene.2014.00211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/19/2014] [Indexed: 12/18/2022] Open
Abstract
A quantitative trait locus (QTL) in the nematode C. elegans, “lsq4,” was recently implicated by mapping longevity genes. QTLs for lifespan and three stress-resistance traits coincided within a span of <300 kbp, later narrowed to <200 kbp. A single gene in this interval is now shown to modulate all lsq4-associated traits. Full-genome analysis of transcript levels indicates that lsq4 contains a dimorphic gene governing the expression of many sperm-specific genes, suggesting an effect on spermatogenesis. Quantitative analysis of allele-specific transcripts encoded within the lsq4 interval revealed significant, 2- to 15-fold expression differences for 10 of 33 genes. Fourteen “dual-candidate” genes, implicated by both position and expression, were tested for RNA-interference effects on QTL-linked traits. In a strain carrying the shorter-lived allele, knockdown of rec-8 (encoding a meiotic cohesin) reduced its transcripts 4-fold, to a level similar to the longer-lived strain, while extending lifespan 25–26%, whether begun before fertilization or at maturity. The short-lived lsq4 allele also conferred sensitivity to oxidative and thermal stresses, and lower male frequency (reflecting X-chromosome non-disjunction), traits reversed uniquely by rec-8 knockdown. A strain bearing the longer-lived lsq4 allele, differing from the short-lived strain at <0.3% of its genome, derived no lifespan or stress-survival benefit from rec-8 knockdown. We consider two possible explanations: high rec-8 expression may include increased “leaky” expression in mitotic cells, leading to deleterious destabilization of somatic genomes; or REC-8 may act entirely in germ-line meiotic cells to reduce aberrations such as non-disjunction, thereby blunting a stress-resistance response mediated by innate immunity. Replicative lifespan was extended 20% in haploid S. cerevisiae (BY4741) by deletion of REC8, orthologous to nematode rec-8, implying that REC8 disruption of mitotic-cell survival is widespread, exemplifying antagonistic pleiotropy (opposing effects on lifespan vs. reproduction), and/or balancing selection wherein genomic disruption increases genetic variation under harsh conditions.
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Affiliation(s)
- Srinivas Ayyadevara
- Central Arkansas Veterans Healthcare System, VA Medical Center Little Rock, AR, USA ; Department of Geriatrics, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Cagdas Tazearslan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - Ramani Alla
- Central Arkansas Veterans Healthcare System, VA Medical Center Little Rock, AR, USA ; Department of Geriatrics, University of Arkansas for Medical Sciences Little Rock, AR, USA
| | - James C Jiang
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center New Orleans, LA, USA
| | - S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center New Orleans, LA, USA
| | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare System, VA Medical Center Little Rock, AR, USA ; Department of Geriatrics, University of Arkansas for Medical Sciences Little Rock, AR, USA ; Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences Little Rock, AR, USA
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21
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Durham MF, Magwire MM, Stone EA, Leips J. Genome-wide analysis in Drosophila reveals age-specific effects of SNPs on fitness traits. Nat Commun 2014; 5:4338. [PMID: 25000897 DOI: 10.1038/ncomms5338] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/09/2014] [Indexed: 12/13/2022] Open
Abstract
Most organisms exhibit senescence; a decline in physiological function with age. In nature, rates of senescence vary extensively among individuals and this variation has a significant genetic component; however, we know little about the genes underlying senescence. Here we show the first evidence that individual alleles influence fecundity in an age-specific manner and so the genetic basis of natural variation in fecundity changes dramatically with age. We complete a genome-wide association to identify single-nucleotide polymorphisms (SNPs) affecting lifespan and age-specific fecundity using the Drosophila melanogaster Genetic Reference Panel. We identify 1,031 SNPs affecting fecundity and 52 influencing lifespan. Only one SNP is associated with both early- and late-age fecundity. The age-specific effect of candidate genes on fecundity is validated using RNA interference. In addition, there is a dramatic increase in the number of SNPs influencing fecundity with age. This result provides support for the mutation accumulation theory of aging.
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Affiliation(s)
- Mary F Durham
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
| | - Michael M Magwire
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Eric A Stone
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
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22
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Knight AL, Yan X, Hamamichi S, Ajjuri RR, Mazzulli JR, Zhang MW, Daigle JG, Zhang S, Borom AR, Roberts LR, Lee SK, DeLeon SM, Viollet-Djelassi C, Krainc D, O'Donnell JM, Caldwell KA, Caldwell GA. The glycolytic enzyme, GPI, is a functionally conserved modifier of dopaminergic neurodegeneration in Parkinson's models. Cell Metab 2014; 20:145-57. [PMID: 24882066 PMCID: PMC4097176 DOI: 10.1016/j.cmet.2014.04.017] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/16/2014] [Accepted: 04/17/2014] [Indexed: 01/05/2023]
Abstract
Neurodegenerative diseases represent an increasing burden in our aging society, yet the underlying metabolic factors influencing onset and progression remain poorly defined. The relationship between impaired IGF-1/insulin-like signaling (IIS) and lifespan extension represents an opportunity to investigate the interface of metabolism with age-associated neurodegeneration. Using data sets of established DAF-2/IIS-signaling components in Caenorhabditis elegans, we conducted systematic RNAi screens in worms to select for daf-2-associated genetic modifiers of α-synuclein misfolding and dopaminergic neurodegeneration, two clinical hallmarks of Parkinson's disease. An outcome of this strategy was the identification of GPI-1/GPI, an enzyme in glucose metabolism, as a daf-2-regulated modifier that acts independent of the downstream cytoprotective transcription factor DAF-16/FOXO to modulate neuroprotection. Subsequent mechanistic analyses using Drosophila and mouse primary neuron cultures further validated the conserved nature of GPI neuroprotection from α-synuclein proteotoxicity. Collectively, these results support glucose metabolism as a conserved functional node at the intersection of proteostasis and neurodegeneration.
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Affiliation(s)
- Adam L Knight
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA; The Babraham Institute, Cambridge CB22 3AT, UK
| | - Xiaohui Yan
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Shusei Hamamichi
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Rami R Ajjuri
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Joseph R Mazzulli
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Mike W Zhang
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - J Gavin Daigle
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Siyuan Zhang
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Akeem R Borom
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Lindsay R Roberts
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - S Kyle Lee
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Susan M DeLeon
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | | | - Dimitri Krainc
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Janis M O'Donnell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kim A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA; Departments of Neurology and Neurobiology, Center for Neurodegeneration and Experimental Therapeutics, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy A Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA; Departments of Neurology and Neurobiology, Center for Neurodegeneration and Experimental Therapeutics, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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23
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Sgrò CM, van Heerwaarden B, Kellermann V, Wee CW, Hoffmann AA, Lee SF. Complexity of the genetic basis of ageing in nature revealed by a clinal study of lifespan and methuselah, a gene for ageing, in Drosophila from eastern Australia. Mol Ecol 2014; 22:3539-51. [PMID: 23802551 DOI: 10.1111/mec.12353] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 03/12/2013] [Accepted: 03/16/2013] [Indexed: 11/29/2022]
Abstract
Clinal studies are a powerful tool for understanding the genetic basis of climatic adaptation. However, while clines in quantitative traits and genetic polymorphisms have been observed within and across continents, few studies have attempted to demonstrate direct links between them. The gene methuselah in Drosophila has been shown to have a major effect on stress response and longevity phenotypes based largely on laboratory studies of induced mutations in the mth gene. Clinal patterns in the most common mth haplotype and for lifespan (both increasing with latitude) have been observed in North American populations of D. melanogaster, implicating climatic selection. While these clinal patterns have led some to suggest that mth influences ageing in natural populations, limited evidence on the association between the two has so far been collected. Here, we describe a significant cline in the mth haplotype in eastern Australian D. melanogaster populations that parallel the cline in North America. We also describe a cline in mth gene expression. These findings further support the idea that mth is itself under selection. In contrast, we show that lifespan has a strong nonlinear clinal pattern, increasing southwards from the tropics, but then decreasing again from mid-latitudes. Furthermore, in association studies, we find no evidence for a direct link between mth haplotype and lifespan. Thus, while our data support a role for mth variation being under natural selection, we found no link to naturally occurring variation in lifespan and ageing in Australian populations of D. melanogaster. Our results indicate that the mth locus likely has genetic background and environment-specific effects.
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Affiliation(s)
- Carla M Sgrò
- Department of Biological Sciences, Monash University, Clayton, Vic., 3800, Australia.
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24
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Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston SL, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders GI, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS, Cotton JA. The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biol 2013; 14:R88. [PMID: 23985316 PMCID: PMC4054779 DOI: 10.1186/gb-2013-14-8-r88] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/27/2013] [Accepted: 08/28/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. RESULTS Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. CONCLUSIONS The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.
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Affiliation(s)
- Roz Laing
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - Taisei Kikuchi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692 Japan
| | - Axel Martinelli
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Isheng J Tsai
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692 Japan
| | - Robin N Beech
- Institute of Parasitology, Macdonald Campus, McGill University, 21,111 Lakeshore Road, Ste. Anne de Bellevue, Québec, Canada H9X 3V9
| | - Elizabeth Redman
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - David J Bartley
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Helen Beasley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Collette Britton
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - David Curran
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Eileen Devaney
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - Aude Gilabert
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Martin Hunt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Frank Jackson
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Stephanie L Johnston
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - Ivan Kryukov
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Keyu Li
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Alison A Morrison
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Adam J Reid
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Neil Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, Scotland, UK
| | - Gary I Saunders
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - James D Wasmuth
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Adrian Wolstenholme
- Department of Infectious Diseases and Center for Tropical and Emerging Global Disease, University of Georgia, Athens, Georgia 30602, USA
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Wang MH, Marinotti O, Zhong D, James AA, Walker E, Guda T, Kweka EJ, Githure J, Yan G. Gene expression-based biomarkers for Anopheles gambiae age grading. PLoS One 2013; 8:e69439. [PMID: 23936017 PMCID: PMC3720620 DOI: 10.1371/journal.pone.0069439] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 06/13/2013] [Indexed: 12/18/2022] Open
Abstract
Information on population age structure of mosquitoes under natural conditions is fundamental to the understanding of vectorial capacity and crucial for assessing the impact of vector control measures on malaria transmission. Transcriptional profiling has been proposed as a method for predicting mosquito age for Aedes and Anopheles mosquitoes, however, whether this new method is adequate for natural conditions is unknown. This study tests the applicability of transcriptional profiling for age-grading of Anopheles gambiae, the most important malaria vector in Africa. The transcript abundance of two An. gambiae genes, AGAP009551 and AGAP011615, was measured during aging under laboratory and field conditions in three mosquito strains. Age-dependent monotonic changes in transcript levels were observed in all strains evaluated. These genes were validated as age-grading biomarkers using the mark, release and recapture (MRR) method. The MRR method determined a good correspondence between actual and predicted age, and thus demonstrated the value of age classifications derived from the transcriptional profiling of these two genes. The technique was used to establish the age structure of mosquito populations from two malaria-endemic areas in western Kenya. The population age structure determined by the transcriptional profiling method was consistent with that based on mosquito parity. This study demonstrates that the transcription profiling method based on two genes is valuable for age determination of natural mosquitoes, providing a new approach for determining a key life history trait of malaria vectors.
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Affiliation(s)
- Mei-Hui Wang
- Program in Public Health, University of California Irvine, Irvine, California, United States of America
- Chao Family Comprehensive Cancer Center, UCI Medical Center, Orange, California, United States of America
| | - Osvaldo Marinotti
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Daibin Zhong
- Program in Public Health, University of California Irvine, Irvine, California, United States of America
| | - Anthony A. James
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
- Department of Microbiology & Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Edward Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Tom Guda
- Human Health Division, International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Eliningaya J. Kweka
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
- Division of Livestock and Human Diseases Vector Control, Tropical Pesticides Research Institute, Ngaramtoni, Arusha, Tanzania
| | - John Githure
- Human Health Division, International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Guiyun Yan
- Program in Public Health, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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26
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Yamamoto R, Bai H, Dolezal AG, Amdam G, Tatar M. Juvenile hormone regulation of Drosophila aging. BMC Biol 2013; 11:85. [PMID: 23866071 PMCID: PMC3726347 DOI: 10.1186/1741-7007-11-85] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 07/05/2013] [Indexed: 01/01/2023] Open
Abstract
Background Juvenile hormone (JH) has been demonstrated to control adult lifespan in a number of non-model insects where surgical removal of the corpora allata eliminates the hormone’s source. In contrast, little is known about how juvenile hormone affects adult Drosophila melanogaster. Previous work suggests that insulin signaling may modulate Drosophila aging in part through its impact on juvenile hormone titer, but no data yet address whether reduction of juvenile hormone is sufficient to control Drosophila life span. Here we adapt a genetic approach to knock out the corpora allata in adult Drosophila melanogaster and characterize adult life history phenotypes produced by reduction of juvenile hormone. With this system we test potential explanations for how juvenile hormone modulates aging. Results A tissue specific driver inducing an inhibitor of a protein phosphatase was used to ablate the corpora allata while permitting normal development of adult flies. Corpora allata knockout adults had greatly reduced fecundity, inhibited oogenesis, impaired adult fat body development and extended lifespan. Treating these adults with the juvenile hormone analog methoprene restored all traits toward wildtype. Knockout females remained relatively long-lived even when crossed into a genotype that blocked all egg production. Dietary restriction further extended the lifespan of knockout females. In an analysis of expression profiles of knockout females in fertile and sterile backgrounds, about 100 genes changed in response to loss of juvenile hormone independent of reproductive state. Conclusions Reduced juvenile hormone alone is sufficient to extend the lifespan of Drosophila melanogaster. Reduced juvenile hormone limits reproduction by inhibiting the production of yolked eggs, and this may arise because juvenile hormone is required for the post-eclosion development of the vitellogenin-producing adult fat body. Our data do not support a mechanism for juvenile hormone control of longevity simply based on reducing the physiological costs of egg production. Nor does the longevity benefit appear to function through mechanisms by which dietary restriction extends longevity. We identify transcripts that change in response to juvenile hormone independent of reproductive state and suggest these represent somatically expressed genes that could modulate how juvenile hormone controls persistence and longevity.
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Affiliation(s)
- Rochele Yamamoto
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
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27
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Fuhrmann J, Mierzwa B, Trentini D, Spiess S, Lehner A, Charpentier E, Clausen T. Structural Basis for Recognizing Phosphoarginine and Evolving Residue-Specific Protein Phosphatases in Gram-Positive Bacteria. Cell Rep 2013; 3:1832-9. [DOI: 10.1016/j.celrep.2013.05.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/07/2013] [Accepted: 05/10/2013] [Indexed: 12/31/2022] Open
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Wit J, Frydenberg J, Sarup P, Loeschcke V. Confirming candidate genes for longevity by RT-qPCR using two different genetic backgrounds and selection methods. JOURNAL OF INSECT PHYSIOLOGY 2013; 59:255-262. [PMID: 23357090 DOI: 10.1016/j.jinsphys.2013.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 06/01/2023]
Abstract
Elucidating genes that affect life span or that can be used as biomarkers for ageing has received attention in diverse studies in recent years. Using model organisms and various approaches several genes have been linked to the longevity phenotype. For Drosophila melanogaster those studies have usually focussed on one sex and on flies originating from one genetic background, and results from different studies often do not overlap. Using D. melanogaster selected for increased longevity we aimed to find robust longevity related genes by examining gene expression in both sexes of flies originating from different genetic backgrounds. Further, we compared expression changes across three ages, when flies were young, middle aged or old, to examine how candidate gene expression changes with the onset of ageing. We selected 10 genes based on their expression differences in prior microarray studies. For about 50% of these we confirmed their potential as a candidate longevity gene. We found one robust candidate gene for longevity, CG32638. Three other genes, CG8934, mRpS10 and Spn43Ad, showed a tendency to be involved in life span determination in both backgrounds tested.
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Affiliation(s)
- Janneke Wit
- Department of Bioscience, Integrative Ecology and Evolution, Aarhus University, NyMunkegade 114-116, DK-8000 Aarhus C, Denmark.
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Wilson RH, Lai CQ, Lyman RF, Mackay TFC. Genomic response to selection for postponed senescence in Drosophila. Mech Ageing Dev 2012; 134:79-88. [PMID: 23262286 DOI: 10.1016/j.mad.2012.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/01/2012] [Accepted: 11/16/2012] [Indexed: 01/25/2023]
Abstract
Limited lifespan and senescence are quantitative traits, controlled by many interacting genes with individually small and environmentally plastic effects, complicating genetic analysis. We performed genome wide analysis of gene expression for two Drosophila melanogaster lines selected for postponed senescence and one control, unselected line to identify candidate genes affecting lifespan as well as variation in lifespan. We obtained gene expression profiles for young flies of all lines, all lines at the time only 10% of the control lines survived, and the time at which 10% of the selected lines survived. Transcriptional responses to aging involved 19% of the genome. The transcriptional signature of aging involved the down-regulation of genes affecting proteolysis, metabolism, oxidative phosphorylation, and mitochrondrial function; and the up-regulation of genes affecting protein synthesis, immunity, defense responses, and the detoxification of xenobiotic substances. The transcriptional signature of postponed senescence involved the up-regulation of proteases and phosphatases and genes affecting detoxification of xenobiotics; and the down-regulation of genes affecting immunity, defense responses, metabolism and muscle function. Functional tests of 17 mutations confirmed 12 novel genes affecting Drosophila lifespan. Identification of genes affecting longevity by analysis of gene expression changes in lines selected for postponed senescence thus complements alternative genetic approaches.
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Affiliation(s)
- Rhonda H Wilson
- Department of Genetics and W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695-7614, United States
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Joy TK, Jeffrey Gutierrez EH, Ernst K, Walker KR, Carriere Y, Torabi M, Riehle MA. Aging field collected Aedes aegypti to determine their capacity for dengue transmission in the southwestern United States. PLoS One 2012; 7:e46946. [PMID: 23077536 PMCID: PMC3470585 DOI: 10.1371/journal.pone.0046946] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 09/10/2012] [Indexed: 11/18/2022] Open
Abstract
Aedes aegypti, the primary vector of dengue virus, is well established throughout urban areas of the Southwestern US, including Tucson, AZ. Local transmission of the dengue virus, however, has not been reported in this area. Although many factors influence the distribution of the dengue virus, we hypothesize that one contributing factor is that the lifespan of female Ae. aegypti mosquitoes in the Southwestern US is too short for the virus to complete development and be transmitted to a new host. To test this we utilized two age grading techniques. First, we determined parity by analyzing ovarian tracheation and found that only 40% of Ae. aegypti females collected in Tucson, AZ were parous. The second technique determined transcript levels of an age-associated gene, Sarcoplasmic calcium-binding protein 1 (SCP-1). SCP-1 expression decreased in a predictable manner as the age of mosquitoes increased regardless of rearing conditions and reproductive status. We developed statistical models based on parity and SCP-1 expression to determine the age of individual, field collected mosquitoes within three age brackets: nonvectors (0-5 days post-emergence), unlikely vectors (6-14 days post-emergence), and potential vectors (15+ days post-emergence). The statistical models allowed us to accurately group individual wild mosquitoes into the three age brackets with high confidence. SCP-1 expression levels of individual, field collected mosquitoes were analyzed in conjunction with parity status. Based on SCP-1 transcript levels and parity data, 9% of collected mosquitoes survived more than 15 days post emergence.
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Affiliation(s)
- Teresa K. Joy
- Department of Entomology, University of Arizona, Tucson, Arizona, United States of America
| | | | - Kacey Ernst
- College of Public Health, University of Arizona, Tucson, Arizona, United States of America
| | - Kathleen R. Walker
- Department of Entomology, University of Arizona, Tucson, Arizona, United States of America
| | - Yves Carriere
- Department of Entomology, University of Arizona, Tucson, Arizona, United States of America
| | - Mohammad Torabi
- Research Computing Principal, University of Arizona, Tucson, Arizona, United States of America
| | - Michael A. Riehle
- Department of Entomology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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31
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Ferreiro MJ, Rodríguez-Ezpeleta N, Pérez C, Hackenberg M, Aransay AM, Barrio R, Cantera R. Whole transcriptome analysis of a reversible neurodegenerative process in Drosophila reveals potential neuroprotective genes. BMC Genomics 2012; 13:483. [PMID: 22978642 PMCID: PMC3496630 DOI: 10.1186/1471-2164-13-483] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 09/11/2012] [Indexed: 01/07/2023] Open
Abstract
Background Neurodegenerative diseases are progressive and irreversible and they can be initiated by mutations in specific genes. Spalt-like genes (Sall) encode transcription factors expressed in the central nervous system. In humans, SALL mutations are associated with hereditary syndromes characterized by mental retardation, sensorineural deafness and motoneuron problems, among others. Drosophila sall mutants exhibit severe neurodegeneration of the central nervous system at embryonic stage 16, which surprisingly reverts later in development at embryonic stage 17, suggesting a potential to recover from neurodegeneration. We hypothesize that this recovery is mediated by a reorganization of the transcriptome counteracting SALL lost. To identify genes associated to neurodegeneration and neuroprotection, we used mRNA-Seq to compare the transcriptome of Drosophila sall mutant and wild type embryos from neurodegeneration and reversal stages. Results Neurodegeneration stage is associated with transcriptional changes in 220 genes, of which only 5% were already described as relevant for neurodegeneration. Genes related to the groups of Redox, Lifespan/Aging and Mitochondrial diseases are significantly represented at this stage. By contrast, neurodegeneration reversal stage is associated with significant changes in 480 genes, including 424 not previously associated with neuroprotection. Immune response and Salt stress are the most represented groups at this stage. Conclusions We identify new genes associated to neurodegeneration and neuroprotection by using an mRNA-Seq approach. The strong homology between Drosophila and human genes raises the possibility to unveil novel genes involved in neurodegeneration and neuroprotection also in humans.
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32
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Liu J, Srinivasan P, Pham DN, Rozovsky S. Expression and purification of the membrane enzyme selenoprotein K. Protein Expr Purif 2012; 86:27-34. [PMID: 22963794 DOI: 10.1016/j.pep.2012.08.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/18/2012] [Accepted: 08/20/2012] [Indexed: 12/18/2022]
Abstract
Selenoprotein K (SelK) is a membrane protein residing in the endoplasmic reticulum. The function of SelK is mostly unknown; however, it has been shown to participate in anti-oxidant defense, calcium regulation and in the endoplasmic reticulum associated protein degradation (ERAD) pathway. In order to study the function of SelK and the role of selenocysteine in catalysis, we have tested heterologous expression of human SelK in E. coli. Consequently, we have developed an over-expression strategy that exploits the maltose binding protein as a fusion partner to stabilize and solubilize SelK. The fusion partner can be cleaved from SelK in the presence of a variety of detergents compatible with structural characterization and the protein purified to homogeneity. SelK acquires a helical secondary structure in detergent micelles, even though it was predicted to be an intrinsically disordered protein due to its high percentage of polar residues. The same strategy was successfully applied to preparation of SelK binding partner - selenoprotein S (SelS). Hence, this heterologous expression and purification strategy can be applied to other members of the membrane enzyme family to which SelK belongs.
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Affiliation(s)
- Jun Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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33
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Shmookler Reis RJ. Coming to terms with complexity: limits to a reductionist view of aging. Front Genet 2012; 3:149. [PMID: 22969788 PMCID: PMC3427912 DOI: 10.3389/fgene.2012.00149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 07/26/2012] [Indexed: 11/17/2022] Open
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34
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Remolina SC, Chang PL, Leips J, Nuzhdin SV, Hughes KA. Genomic basis of aging and life-history evolution in Drosophila melanogaster. Evolution 2012; 66:3390-403. [PMID: 23106705 DOI: 10.1111/j.1558-5646.2012.01710.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural diversity in aging and other life-history patterns is a hallmark of organismal variation. Related species, populations, and individuals within populations show genetically based variation in life span and other aspects of age-related performance. Population differences are especially informative because these differences can be large relative to within-population variation and because they occur in organisms with otherwise similar genomes. We used experimental evolution to produce populations divergent for life span and late-age fertility and then used deep genome sequencing to detect sequence variants with nucleotide-level resolution. Several genes and genome regions showed strong signatures of selection, and the same regions were implicated in independent comparisons, suggesting that the same alleles were selected in replicate lines. Genes related to oogenesis, immunity, and protein degradation were implicated as important modifiers of late-life performance. Expression profiling and functional annotation narrowed the list of strong candidate genes to 38, most of which are novel candidates for regulating aging. Life span and early age fecundity were negatively correlated among populations; therefore, the alleles we identified also are candidate regulators of a major life-history trade-off. More generally, we argue that hitchhiking mapping can be a powerful tool for uncovering the molecular bases of quantitative genetic variation.
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Affiliation(s)
- Silvia C Remolina
- Department of Animal Biology, University of Illinois, Urbana-Champaign, 505 S. Goodwin Ave, Urbana, Illinois 61801, USA
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35
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Age-specific variation in immune response in Drosophila melanogaster has a genetic basis. Genetics 2012; 191:989-1002. [PMID: 22554890 DOI: 10.1534/genetics.112.140640] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Immunosenescence, the age-related decline in immune system function, is a general hallmark of aging. While much is known about the cellular and physiological changes that accompany immunosenescence, we know little about the genetic influences on this phenomenon. In this study we combined age-specific measurements of bacterial clearance ability following infection with whole-genome measurements of the transcriptional response to infection and wounding to identify genes that contribute to the natural variation in immunosenescence, using Drosophila melanogaster as a model system. Twenty inbred lines derived from nature were measured for their ability to clear an Escherichia coli infection at 1 and 4 weeks of age. We used microarrays to simultaneously determine genome-wide expression profiles in infected and wounded flies at each age for 12 of these lines. Lines exhibited significant genetically based variation in bacterial clearance at both ages; however, the genetic basis of this variation changed dramatically with age. Variation in gene expression was significantly correlated with bacterial clearance ability only in the older age group. At 4 weeks of age variation in the expression of 247 genes following infection was associated with genetic variation in bacterial clearance. Functional annotation analyses implicate genes involved in energy metabolism including those in the insulin signaling/TOR pathway as having significant associations with bacterial clearance in older individuals. Given the evolutionary conservation of the genes involved in energy metabolism, our results could have important implications for understanding immunosenescence in other organisms, including humans.
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36
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Bergland AO, Chae HS, Kim YJ, Tatar M. Fine-scale mapping of natural variation in fly fecundity identifies neuronal domain of expression and function of an aquaporin. PLoS Genet 2012; 8:e1002631. [PMID: 22509142 PMCID: PMC3320613 DOI: 10.1371/journal.pgen.1002631] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 02/20/2012] [Indexed: 11/29/2022] Open
Abstract
To gain insight into the molecular genetic basis of standing variation in fitness related traits, we identify a novel factor that regulates the molecular and physiological basis of natural variation in female Drosophila melanogaster fecundity. Genetic variation in female fecundity in flies derived from a wild orchard population is heritable and largely independent of other measured life history traits. We map a portion of this variation to a single QTL and then use deficiency mapping to further refine this QTL to 5 candidate genes. Ubiquitous expression of RNAi against only one of these genes, an aquaporin encoded by Drip, reduces fecundity. Within our mapping population Drip mRNA level in the head, but not other tissues, is positively correlated with fecundity. We localize Drip expression to a small population of corazonin producing neurons located in the dorsolateral posterior compartments of the protocerebrum. Expression of Drip–RNAi using both the pan-neuronal ELAV-Gal4 and the Crz-Gal4 drivers reduces fecundity. Low-fecundity RILs have decreased Crz expression and increased expression of pale, the enzyme encoding the rate-limiting step in the production of dopamine, a modulator of insect life histories. Taken together these data suggest that natural variation in Drip expression in the corazonin producing neurons contributes to standing variation in fitness by altering the concentration of two neurohormones. A major goal of modern evolutionary biology is to elucidate the genetic basis of standing genetic variation underlying fitness traits. This goal is important for a comprehensive picture of the evolutionary process, because it allows us to understand the mode of natural selection on fitness traits and identify the molecular and physiological processes that affect fitness traits. Here, we describe our work to identify the molecular genetic and physiological basis for natural variation in a core life history trait, fecundity, of Drosophila melanogaster. Using a variety of mapping techniques, we show that differential expression of the aquaporin Drip in nervous tissue affects natural variation in female fecundity. We further go on to describe a novel domain of expression of Drip in neurons that produce the insect stress hormone corazonin and demonstrate that differential expression of Drip in these neurons affects female fecundity putatively through modulating the concentration of corazonin and dopamine. This surprising and novel observation highlights the benefit of exploiting natural genetic variation to identify the molecular processes underlying phenotypic traits.
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Affiliation(s)
- Alan O Bergland
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, USA.
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37
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Kirschner J, Weber D, Neuschl C, Franke A, Böttger M, Zielke L, Powalsky E, Groth M, Shagin D, Petzold A, Hartmann N, Englert C, Brockmann GA, Platzer M, Cellerino A, Reichwald K. Mapping of quantitative trait loci controlling lifespan in the short-lived fish Nothobranchius furzeri--a new vertebrate model for age research. Aging Cell 2012; 11:252-61. [PMID: 22221414 PMCID: PMC3437503 DOI: 10.1111/j.1474-9726.2011.00780.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The African annual fish Nothobranchius furzeri emerged as a new model for age research over recent years. Nothobranchius furzeri show an exceptionally short lifespan, age-dependent cognitive/behavioral decline, expression of age-related biomarkers, and susceptibility to lifespan manipulation. In addition, laboratory strains differ largely in lifespan. Here, we set out to study the genetics of lifespan determination. We crossed a short- to a long-lived strain, recorded lifespan, and established polymorphic markers. On the basis of genotypes of 411 marker loci in 404 F(2) progeny, we built a genetic map comprising 355 markers at an average spacing of 5.5 cM, 22 linkage groups (LGs) and 1965 cM. By combining marker data with lifespan values, we identified one genome-wide highly significant quantitative trait locus (QTL) on LG 9 (P < 0.01), which explained 11.3% of the F(2) lifespan variance, and three suggestive QTLs on LG 11, 14, and 17. We characterized the highly significant QTL by synteny analysis, because a genome sequence of N. furzeri was not available. We located the syntenic region on medaka chromosome 5, identified candidate genes, and performed fine mapping, resulting in a c. 40% reduction of the initial 95% confidence interval. We show both that lifespan determination in N. furzeri is polygenic, and that candidate gene detection is easily feasible by cross-species analysis. Our work provides first results on the way to identify loci controlling lifespan in N. furzeri and illustrates the potential of this vertebrate species as a genetic model for age research.
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Affiliation(s)
- Jeanette Kirschner
- Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
| | - David Weber
- Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
| | - Christina Neuschl
- Faculty of Agriculture and Horticulture, Department of Crop and Animal Sciences, Humboldt‐University, Berlin, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian‐Albrechts‐University, Kiel, Germany
| | - Marco Böttger
- Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
| | - Lea Zielke
- Faculty of Agriculture and Horticulture, Department of Crop and Animal Sciences, Humboldt‐University, Berlin, Germany
| | - Eileen Powalsky
- Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
| | - Marco Groth
- Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
| | - Dmitry Shagin
- Evrogen JSC, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Andreas Petzold
- Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
| | - Nils Hartmann
- Molecular Genetics, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
| | - Christoph Englert
- Molecular Genetics, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
| | - Gudrun A. Brockmann
- Faculty of Agriculture and Horticulture, Department of Crop and Animal Sciences, Humboldt‐University, Berlin, Germany
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
| | - Alessandro Cellerino
- Biology of Aging, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
- Scuola Normale Superiore, Pisa, Italy
| | - Kathrin Reichwald
- Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
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Shmookler Reis RJ, Ayyadevara S, Crow WA, Lee T, Delongchamp RR. Gene categories differentially expressed in C. elegans age-1 mutants of extraordinary longevity: new insights from novel data-mining procedures. J Gerontol A Biol Sci Med Sci 2011; 67:366-75. [PMID: 22021389 DOI: 10.1093/gerona/glr186] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Two nonsense mutants of age-1, the Caenorhabditis elegans gene encoding phosphoinositide 3-kinase, live nearly 10-fold longer than wild-type controls and are exceptionally resistant to several stresses. Genome-wide expression analyses implicated downregulation of many more genes than were upregulated in second-generation age-1 homozygotes. Functional-annotation analysis, based on Gene Ontology terms, suggested that novel mechanisms may mediate the stronger phenotypes observed for these worms than with milder age-1 disruption. For the current study, the same microarray data were reanalyzed using novel meta-analytic procedures that we developed recently. First, gene p values were corrected for systematic biases based on the observed distribution for nonexpressed genes; these values were then combined to derive an aggregate p value for each functional-annotation term while adjusting for intergene covariance. This resulted in much better coverage of relevant gene categories, including many that were independently supported by other data. The number of nonredundant GO categories significantly distinguishing age-1 alleles of exceptional longevity increased from sevenfold to greater than ninefold, improving both sensitivity and specificity of selection for altered pathways and implicating previously unsuspected longevity mechanisms. Of 150 genes whose differential expression underlay significant GO terms in both comparisons, over half were up- or down-regulated in accord with longevity, whereas one third showed altered expression uniquely in the longest-lived age-1-null strains, consistent with the activation or suppression of pathways peculiar to strong age-1 mutants.
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Defays R, Gómez FH, Sambucetti P, Scannapieco AC, Loeschcke V, Norry FM. Quantitative trait loci for longevity in heat-stressed Drosophila melanogaster. Exp Gerontol 2011; 46:819-26. [PMID: 21798333 DOI: 10.1016/j.exger.2011.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 06/04/2011] [Accepted: 07/11/2011] [Indexed: 02/02/2023]
Abstract
Longevity is a typical quantitative trait which is influenced by multiple genes. Here we explore the genetic variation in longevity of Drosophila melanogaster in both mildly heat-stressed and control flies. Quantitative trait loci (QTL) analysis for longevity was performed in a single-sex environment at 25°C with and without a mild heat-stress pre-treatment, using a previously reported set of recombinant inbred lines (RIL). QTL regions for longevity in heat-stressed flies overlapped with QTL for longevity in control flies. All longevity QTL co-localized with QTL for longevity identified in previous studies using very different sets of RIL in mixed sex environments, though the genome is nearly saturated with QTL for longevity when considering all previous studies. Heat stress decreased the number of significant QTL for longevity if compared to the control environment. Our mild heat-stress pre-treatment had a beneficial effect (hormesis) more often in shorter-lived than in longer-lived RIL.
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Affiliation(s)
- Raquel Defays
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, (C-1428-EHA) Buenos Aires, Argentina
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41
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Wang MH, Marinotti O, James AA, Walker E, Githure J, Yan G. Genome-wide patterns of gene expression during aging in the African malaria vector Anopheles gambiae. PLoS One 2010; 5:e13359. [PMID: 20967211 PMCID: PMC2954169 DOI: 10.1371/journal.pone.0013359] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 09/15/2010] [Indexed: 11/23/2022] Open
Abstract
The primary means of reducing malaria transmission is through reduction in longevity in days of the adult female stage of the Anopheles vector. However, assessing chronological age is limited to crude physiologic methods which categorize the females binomially as either very young (nulliparous) or not very young (parous). Yet the epidemiologically relevant reduction in life span falls within the latter category. Age-grading methods that delineate chronological age, using accurate molecular surrogates based upon gene expression profiles, will allow quantification of the longevity-reducing effects of vector control tools aimed at the adult, female mosquito. In this study, microarray analyses of gene expression profiles in the African malaria vector Anopheles gambiae were conducted during natural senescence of females in laboratory conditions. Results showed that detoxification-related and stress-responsive genes were up-regulated as mosquitoes aged. A total of 276 transcripts had age-dependent expression, independently of blood feeding and egg laying events. Expression of 112 (40.6%) of these transcripts increased or decreased monotonically with increasing chronologic age. Seven candidate genes for practical age assessment were tested by quantitative gene amplification in the An. gambiae G3 strain in a laboratory experiment and the Mbita strain in field enclosures set up in western Kenya under conditions closely resembling natural ones. Results were similar between experiments, indicating that senescence is marked by changes in gene expression and that chronological age can be gauged accurately and repeatedly with this method. These results indicate that the method may be suitable for accurate gauging of the age in days of field-caught, female An. gambiae.
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Affiliation(s)
- Mei-Hui Wang
- Program in Public Health, University of California Irvine, Irvine, California, United States of America
| | - Osvaldo Marinotti
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Anthony A. James
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, United States of America
| | - Edward Walker
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - John Githure
- Division of Human Health, International Centre of Insect Physiology and Ecology (ICIPE), Nairobi, Kenya
| | - Guiyun Yan
- Program in Public Health, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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42
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Magwire MM, Yamamoto A, Carbone MA, Roshina NV, Symonenko AV, Pasyukova EG, Morozova TV, Mackay TFC. Quantitative and molecular genetic analyses of mutations increasing Drosophila life span. PLoS Genet 2010; 6:e1001037. [PMID: 20686706 PMCID: PMC2912381 DOI: 10.1371/journal.pgen.1001037] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 06/23/2010] [Indexed: 01/21/2023] Open
Abstract
Understanding the genetic and environmental factors that affect variation in life span and senescence is of major interest for human health and evolutionary biology. Multiple mechanisms affect longevity, many of which are conserved across species, but the genetic networks underlying each mechanism and cross-talk between networks are unknown. We report the results of a screen for mutations affecting Drosophila life span. One third of the 1,332 homozygous P-element insertion lines assessed had quantitative effects on life span; mutations reducing life span were twice as common as mutations increasing life span. We confirmed 58 mutations with increased longevity, only one of which is in a gene previously associated with life span. The effects of the mutations increasing life span were highly sex-specific, with a trend towards opposite effects in males and females. Mutations in the same gene were associated with both increased and decreased life span, depending on the location and orientation of the P-element insertion, and genetic background. We observed substantial--and sex-specific--epistasis among a sample of ten mutations with increased life span. All mutations increasing life span had at least one deleterious pleiotropic effect on stress resistance or general health, with different patterns of pleiotropy for males and females. Whole-genome transcript profiles of seven of the mutant lines and the wild type revealed 4,488 differentially expressed transcripts, 553 of which were common to four or more of the mutant lines, which include genes previously associated with life span and novel genes implicated by this study. Therefore longevity has a large mutational target size; genes affecting life span have variable allelic effects; alleles affecting life span exhibit antagonistic pleiotropy and form epistatic networks; and sex-specific mutational effects are ubiquitous. Comparison of transcript profiles of long-lived mutations and the control line reveals a transcriptional signature of increased life span.
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Affiliation(s)
- Michael M Magwire
- Department of Genetics and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina, United States of America
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Seong KM, Kim CS, Seo SW, Jeon HY, Lee BS, Nam SY, Yang KH, Kim JY, Kim CS, Min KJ, Jin YW. Genome-wide analysis of low-dose irradiated male Drosophila melanogaster with extended longevity. Biogerontology 2010; 12:93-107. [DOI: 10.1007/s10522-010-9295-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 06/25/2010] [Indexed: 01/06/2023]
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Lai CQ, Parnell LD, Troen AM, Shen J, Caouette H, Warodomwichit D, Lee YC, Crott JW, Qiu WQ, Rosenberg IH, Tucker KL, Ordovás JM. MAT1A variants are associated with hypertension, stroke, and markers of DNA damage and are modulated by plasma vitamin B-6 and folate. Am J Clin Nutr 2010; 91:1377-86. [PMID: 20335551 PMCID: PMC2854908 DOI: 10.3945/ajcn.2009.28923] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The S-adenosylmethionine synthetase type 1 (MAT1A) gene encodes a key enzyme in one-carbon nutrient metabolism. OBJECTIVE This study aimed to determine the association of MAT1A variants with homocysteine, DNA damage, and cardiovascular disease (CVD). DESIGN Eight variants of MAT1A were examined for associations with hypertension, stroke, CVD, homocysteine, and DNA damage in 1006 participants of the Boston Puerto Rican Health Study. Two variants were replicated in 1147 participants of the Nutrition, Aging, and Memory in Elders Study. RESULTS Two variants and haplotypes were strongly associated with hypertension and stroke, independent of methylenetetrahydrofolate reductase (MTHFR) variants. Homozygotes of the MAT1A d18777A (rs3851059) allele had a significantly greater likelihood of stroke (odds ratio: 4.30; 95% CI: 1.34, 12.19; P = 0.006), whereas 3U1510A (rs7087728) homozygotes had a lower likelihood of hypertension (odds ratio: 0.67; 95% CI: 0.48, 0.95; P = 0.022) and stroke (odds ratio: 0.35; 95% CI: 0.15, 0.82; P = 0.015). A similar trend of association was observed in a second elderly population. Furthermore, strong interactions between MAT1A genotypes and vitamin B-6 status were found. Carriers of the nonrisk allele 3U1510A had a lower 8-hydroxydeoxyguanosine concentration--a biomarker of oxidative DNA damage--when plasma vitamin B-6 was high, whereas homozygotes for the risk-allele 3U1510G had higher 8-hydroxydeoxyguanosine concentrations, regardless of vitamin B-6 status. CONCLUSIONS MAT1A variants were strongly associated with hypertension and stroke. Improving folate and vitamin B-6 status might decrease the CVD risk of only a subset of the population, depending on genotype. These findings suggest that impairments in methylation activity, independent of homocysteine, have an effect on CVD risk.
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Affiliation(s)
- Chao-Qiang Lai
- Nutrition and Genomics Laboratory, Jean Mayer-US Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA.
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Kocher SD, Tarpy DR, Grozinger CM. The effects of mating and instrumental insemination on queen honey bee flight behaviour and gene expression. INSECT MOLECULAR BIOLOGY 2010; 19:153-62. [PMID: 20002808 PMCID: PMC2989600 DOI: 10.1111/j.1365-2583.2009.00965.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Mating is fundamental to most organisms, although the physiological and transcriptional changes associated with this process have been largely characterized only in Drosophila melanogaster. In this study, we use honey bees as a model system because their queens undergo massive and permanent physiological and behavioural changes following mating. Previous studies have identified changes associated with the transition from a virgin queen to a fully mated, egg-laying queen. Here, we further uncouple the mating process to examine the effects of natural mating vs. instrumental insemination and saline vs. semen insemination. We observed effects on flight behaviour, vitellogenin expression and significant overlap in transcriptional profiles between our study and analogous studies in D. melanogaster, suggesting that some post-mating mechanisms are conserved across insect orders.
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Affiliation(s)
- S D Kocher
- Department of Genetics, North Carolina State University, Raleigh, NC 27695, USA.
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46
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Gene expression profiling implicates OXPHOS complexes in lifespan extension of flies over-expressing a small mitochondrial chaperone, Hsp22. Exp Gerontol 2009; 45:611-20. [PMID: 20036725 DOI: 10.1016/j.exger.2009.12.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 12/16/2009] [Accepted: 12/17/2009] [Indexed: 11/23/2022]
Abstract
Aging is a complex process accompanied by a decreased capacity to tolerate and respond to various stresses. Heat shock proteins as part of cell defense mechanisms are up-regulated following stress. In Drosophila, the mitochondrial Hsp22 is preferentially up-regulated in aged flies. Its over-expression results in an extension of lifespan and an increased resistance to stress. Hsp22 has chaperone-like activity in vitro, but the mechanism(s) by which it increases lifespan in flies are unknown. Genome-wide analysis was performed on long-lived Hsp22+ and control flies to unveil transcriptional changes brought by Hsp22. Transcriptomes obtained at 45days, 90% and 50% survival were then compared between them to focus more on genes up- or down-regulated in presence of higher levels of hsp22 mRNA. Hsp22+ flies display an up-regulation of genes mainly related to mitochondrial energy production and protein biosynthesis, two functions normally down-regulated during aging. Interestingly, among the 26 genes up-regulated in Hsp22+ flies, 7 genes encode for mitochondrial proteins, 5 of which being involved in OXPHOS complexes. Other genes that could influence aging such as CG5002, dGCC185 and GstS1 also displayed a regulation linked to Hsp22 expression. The up-regulation of genes of the OXPHOS system in Hsp22+ flies suggest that mitochondrial homeostasis is at the center of Hsp22 beneficial effects on lifespan.
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47
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Pb2+: an endocrine disruptor in Drosophila? Physiol Behav 2009; 99:254-9. [PMID: 19800356 DOI: 10.1016/j.physbeh.2009.09.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 09/10/2009] [Accepted: 09/17/2009] [Indexed: 11/24/2022]
Abstract
Environmental exposure to Pb(2+) affects hormone-mediated responses in vertebrates. To help establish the fruit fly, Drosophila melanogaster, as a model system for studying such disruption, we describe effects of Pb(2+) on hormonally regulated traits. These include duration of development, longevity, females' willingness to mate, fecundity and adult locomotor activity. Developmental Pb(2+) exposure has been shown to affect gene expression in a specific region of the Drosophila genome (approximately 122 genes) involved in lead-induced changes in adult locomotion and to affect regulation of intracellular calcium levels associated with neuronal activity at identified synapses in the larval neuromuscular junction. We suggest ways in which Drosophila could become a new model system for the study of endocrine disruptors at genetic, neural and behavioral levels of analysis, particularly by use of genomic methods. This will facilitate efforts to distinguish between behavioral effects of Pb(2+) caused by direct action on neural mechanisms versus effects of Pb(+2) on behavior mediated through endocrine disruption.
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48
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Rand MD. Drosophotoxicology: the growing potential for Drosophila in neurotoxicology. Neurotoxicol Teratol 2009; 32:74-83. [PMID: 19559084 DOI: 10.1016/j.ntt.2009.06.004] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 05/26/2009] [Accepted: 06/08/2009] [Indexed: 02/04/2023]
Abstract
Understanding neurotoxic mechanisms is a challenge of deciphering which genes and gene products in the developing or mature nervous system are targeted for disruption by chemicals we encounter in our environment. Our understanding of nervous system development and physiology is highly advanced due in large part to studies conducted in simple non-mammalian models. The paucity of toxicological data for the more than 80,000 chemicals in commercial use today, and the approximately 2000 new chemicals introduced each year, makes development of sensitive and rapid assays to screen for neurotoxicity paramount. In this article I advocate the use of Drosophila in the modern regimen of toxicological testing, emphasizing its unique attributes for assaying neurodevelopment and behavior. Features of the Drosophila model are reviewed and a generalized overall scheme for its use in toxicology is presented. Examples of where the fly has proven fruitful in evaluating common toxicants in our environment are also highlighted. Attention is drawn to three areas where development and application of the fly model might benefit toxicology the most: 1) optimizing sensitive endpoints for pathway-specific screening, 2) accommodating high throughput demands for analysis of chemical toxicant libraries, 3) optimizing genetic and molecular protocols for more rapid identification toxicant-by-gene interactions. While there are shortcomings in the Drosophila model, which exclude it from effective toxicological testing in certain arenas, conservation of fundamental cellular and developmental mechanisms between flies and man is extensive enough to warrant a central role for the Drosophila model in toxicological testing of today.
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Affiliation(s)
- Matthew D Rand
- Department of Anatomy and Neurobiology, College of Medicine, University of Vermont, Burlington, VT 05405, USA.
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Abstract
Aggressive behavior is observed across animal taxa and is likely to be evolutionarily conserved. Although potentially advantageous, aggression can have social and health consequences in humans, and is a component of a number of psychiatric disorders. As a complex genetic trait, it is modulated by numerous quantitative trait loci (QTL) with allelic effects that can vary in direction and magnitude and that are sensitive to environmental perturbations. Assays to quantify aggressive behavior in Drosophila melanogaster have been developed, making this an ideal model system in which to dissect the genomic architecture underlying manifestation of and variation in aggressive behavior. Here, we map QTL affecting variation in aggression between two wild-type Drosophila strains. We identified a minimum of five QTL in a genomewide scan: two on chromosome 2 and three on chromosome 3. At least three and possibly all five of these QTL interact epistatically. We used deficiency complementation mapping to subdivide two linked, epistatically interacting QTL of large effect on chromosome 3 into at least six QTL, and complementation tests to mutations identified four candidate quantitative trait genes. Extensive epistasis poses a serious challenge for understanding the genetic basis of complex traits.
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50
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Abstract
Several possible and potentially overlapping genetic mechanisms have been suggested to explain differences in life span between males and females. Two recent papers in BMC Evolutionary Biology on the effects of inbreeding provide additional insight into the genetic architecture underlying life span differences between genders in two different insects.
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Affiliation(s)
- John Tower
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.
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